User: Ghani

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Ghani0
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Posts by Ghani

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Comment: C: How to extract only transition mutations/ SNPs from VCF file
... All this would do is extract positions where the REF allele is G and ALT is C irrespective of your subject ‘s genotype. It will NOT give you positions where your subject has G > C mutations ...
written 3 months ago by Ghani0
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Comment: C: Transversion vs Transition sites
... It is most relevant to Bioinformatics since you always see reference made to Ti/Tv ratio as a quality control statistic in sequence processing. You also have many researchers that use "transversion" only sites in downstream analysis because they think that those are more stable sites and less subje ...
written 3 months ago by Ghani0
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Transversion vs Transition sites
... Is there anyone besides me who thinks it is foolish to label sites as Transversion or Transition. I mean what determines whether a site is a transition or transversion site since nucleotides are free to mutate to anything. For example if we have an A on the + strand (T - strand), then the A is free ...
genome sequence snp written 3 months ago by Ghani0
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Comment: C: Strategy for processing ancient DNA
... With regards to optimizing settings on HaplotypeCaller: Besides setting --minPruning and --minDanglingBranchLength to 1, so as to not throw out any branch of the graph that has less than 2 reads during realignment, since default minPruning is 2, and since length of a dangling branch to attempt reco ...
written 12 months ago by Ghani0
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Strategy for processing ancient DNA
... Hi everyone, My favorite caller with regards to true and false positive variant results is HaplotypeCaller combined with BWA mem for mapping. This is based on personal experience using Freebayes and bcftools, but I have not compared haplotypecaller with callers such as STSchiff which is specificall ...
haplotypecaller adna written 12 months ago by Ghani0 • updated 11 months ago by the_smiao0
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Comment: C: Diploid vs Haploid calls
... Thanks Brian, by single strand library, I mean those ancient DNA cases where the 2 strands are seperated and only 1 strand is sequenced.. In this situation would'nt it be better to tell the caller to make haploid calls, and if so what commands would you use with GATK Haplotypecaller. I have used BC ...
written 12 months ago by Ghani0
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Comment: C: Diploid vs Haploid calls
... I think what you are thinking is consistent with what I said. Best to illustrate with an example: Let's assume that the sequenced locus is actually C/T. What we likely hopefully see assuming a read depth of 20 at that position, is approximatley 10 C reads and 10 T reads (correct me if I'm wrong). ...
written 12 months ago by Ghani0
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Diploid vs Haploid calls
... Hi everyone, My question is a basic one, but very important to understanding how sequence processing actually works. What determines (how does a variant calling program know) whether a specific locus in a sequenced dna fragment should be diploid (e.g A/T or C/G) or haploid (e.g C/C, T/T). Is it b ...
assembly alignment sequencing written 12 months ago by Ghani0 • updated 12 months ago by Brian Bushnell15k

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